7-127615029-C-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001366110.1(PAX4):c.211G>T(p.Gly71Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000206 in 1,614,220 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001366110.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PAX4 | ENST00000639438.3 | c.211G>T | p.Gly71Cys | missense_variant | Exon 5 of 12 | 5 | NM_001366110.1 | ENSP00000491782.1 |
Frequencies
GnomAD3 genomes AF: 0.00111 AC: 169AN: 152212Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000282 AC: 71AN: 251402Hom.: 0 AF XY: 0.000191 AC XY: 26AN XY: 135864
GnomAD4 exome AF: 0.000112 AC: 164AN: 1461890Hom.: 1 Cov.: 33 AF XY: 0.0000619 AC XY: 45AN XY: 727248
GnomAD4 genome AF: 0.00111 AC: 169AN: 152330Hom.: 0 Cov.: 32 AF XY: 0.00106 AC XY: 79AN XY: 74478
ClinVar
Submissions by phenotype
Type 2 diabetes mellitus;C2677132:Maturity-onset diabetes of the young type 9 Uncertain:1
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not specified Benign:1
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PAX4-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Monogenic diabetes Benign:1
ACMG Criteria:PP3 (7 predictors), BP4 (3 predictors), BS2 (5 cases and 5 controls in T2DM) -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at